Tracking the establishment of local endemic populations of an emergent enteric pathogen
Holt KE., Thieu Nga TV., Thanh DP., Vinh H., Kim DW., Vu Tra MP., Campbell JI., Hoang NVM., Vinh NT., Minh PV., Thuy CT., Nga TTT., Thompson C., Dung TTN., Nhu NTK., Vinh PV., Tuyet PTN., Phuc HL., Lien NTN., Phu BD., Ai NTT., Tien NM., Dong N., Parry CM., Hien TT., Farrar JJ., Parkhill J., Dougan G., Thomson NR., Baker S.
Significance Shigella sonnei is a globally emerging agent of bacterial dysentery. Here, we use genomics to examine the microevolution of S. sonnei in Vietnam. We show that S. sonnei was introduced into Vietnam in the early 1980s, where it continued to evolve, spreading geographically to establish localized founder populations. The population in Ho Chi Minh City has undergone several localized clonal replacement events, during which a small number of microevolutionary changes have risen to dominance. These changes, induced by horizontal gene transfer and substitution mutations, confer high-level antimicrobial resistance and the ability to kill other gut bacteria. This work provides a unique, high-resolution insight into the microevolution of a pioneering human pathogen during its establishment in a new host population.